April 03, 2011

Rare and common genetic variants in humans

The findings of this paper are not very surprising, but it is nice to see them formally expressed and tested.

Common variants are usually not functional; this makes sense as alleles that differ functionally from their competitors at a given locus are likely to win/lose in the evolutionary game and either become fixed, disappear, or be maintained at an extremely low frequency (and hence not be common).

The finding that major derived alleles are more functional also makes sense: a new allele at a given locus may either disappear, attain a non-trivial frequency by random drift, or even achieve a high frequency, pushing the ancestral allele to a lower one. In the latter case, the derived allele becomes the major (most frequent) allele in the population. A high frequency can be attained by either drift or selection: drift is slow and effective in small populations, whereas selection is faster, depending on the relative advantage of the new allele.

Polymorphism in the human genome can be maintained by either mutation-selection, whereby new variants appear constantly due to mutations in individuals, and selection culls many of them, or by balancing selection, whereby different variants have important functions but involve tradeoffs so that a tug-of-war between them results in an equilibrium.

What this paper suggests is that:

Most common variants are not functional

Common derived variants that are functional attain a high frequency and become the major alleles

Rare variants are more likely to be functional than common ones

Selection operates mostly by the constant culling of new alleles, sometimes by favoring new derived alleles, but, not so much by a tug-of-war between competing alleles

This Lego-block paradigm is based on the notion that most of our alleles are commodity"building blocks"; if they are brought together harmoneously, they produce positive results. The occasional allele may have a large effect, and some alleles fit better together than others. Yet, most of the success or failure of a construction depends on how the components fit together, and not what they are.

That, in my opinion, is where the "hidden heritability" mostly hides: part of it is due to the degradation of function by rare mutations that run in families or small populations, and part of it is due to the fortuitous combination of commodity alleles that have no long-term evolutionary advantage/disadvantage (function), but are co-inherited in the short-term from parents to offspring.

The authors have this to say:

Our analyses suggest that most of the functional variation carried by humans is likely to be rare genetic variation that is at least moderately deleterious and held to low frequency by selection.43,44 These analyses therefore provide a possible explanation for the relatively limited role of common genetic variation in most human diseases identified by genome-wide association studies.1,3

"The more common a variant is, the less likely it is to be found in a functional region of the genome," said senior author David Goldstein, Ph.D., director of the Duke Center for Human Genome Variation. "Scientists have reported this observation before, but this study is the most comprehensive effort to date using annotations of the functional regions of the human genome and fully sequenced genomes."

Goldstein said that "the magnitude of the effect is dramatic and is consistent across all frequencies of variants we looked at." He also said he was surprised by the notable consistency of the finding. "It's not just that the most rare variants are different from the most common, it's that at every increase in frequency, a variant is less and less likely to be found in a functional region of the DNA," Goldstein said. "This analysis is consistent with what appears to be a growing consensus that common variants are less important in common diseases than many had originally thought."

The American Journal of Human Genetics, 31 March 2011

doi:10.1016/j.ajhg.2011.03.008

A Genome-wide Comparison of the Functional Properties of Rare and Common Genetic Variants in Humans

Qianqian Zhu et al.

AbstractOne of the longest running debates in evolutionary biology concerns the kind of genetic variation that is primarily responsible for phenotypic variation in species. Here, we address this question for humans specifically from the perspective of population allele frequency of variants across the complete genome, including both coding and noncoding regions. We establish simple criteria to assess the likelihood that variants are functional based on their genomic locations and then use whole-genome sequence data from 29 subjects of European origin to assess the relationship between the functional properties of variants and their population allele frequencies. We find that for all criteria used to assess the likelihood that a variant is functional, the rarer variants are significantly more likely to be functional than the more common variants. Strikingly, these patterns disappear when we focus on only those variants in which the major alleles are derived. These analyses indicate that the majority of the genetic variation in terms of phenotypic consequence may result from a mutation-selection balance, as opposed to balancing selection, and have direct relevance to the study of human disease.

3 comments:

This study seems to be focused on disease causing, in other words, negative functional genetic variants. It is entirely expected for negative functional genetic variants to be rare, as they will usually be prevented from attaining a high frequency by selection or at least will not be favored by selection to attain a high frequency. But what about positive and neutral functional genetic variants? I am not sure whether they are usually rare too.

Does this study take into account environmentally triggered epigenetic effects? I can believe a common environment would show this result, but that possibly different environments would have different selectors.

There are at least two scenarios in which common variants are functional.

One is the new and emergent allele that arose due to a mutation but has not yet attained fixation.

The other is the "ecological" situation. These apply when a mix of functional traits is more adaptive for the community than a single version of the trait. Genetic influences on normal range personality traits are often viewed as fitting this model. For example, to the extent that it is genetically determined, neither an entirely extroverted, nor an entirely introverted group of people may be optimally adaptive. A society needs lots of team players, but also specialists who devote themselves to solidary acts to gain expertise of use to all and to help the society avoid group think. It needs a mix of risk takers and cautious people.

An example that may be a bit of both of those models may be anxiety. Excessive anxiety is one of the one or two most common mental health conditions today, and likely to be significantly hereditary as it can be identified phenotypically by very early childhood. It is easy to see how excessive fear could have a survival advantage historically, but in our newly safe world, it is maladaptive. Yet, communities entirely full of people paralyzed by fear are maladaptive too. While it is often adaptive to panic and flee from a poisonous spider, someobody has to be suited to serving as an exterminator.

This may be an allele that has historically been common for ecological reasons, but which is also growing rarer as it becomes maladaptive.

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